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Kayili HM, Salih B. Fast and efficient proteolysis by reusable pepsin-encapsulated magnetic sol-gel material for mass spectrometry-based proteomics applications. Talanta 2016; 155:78-86. [DOI: 10.1016/j.talanta.2016.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 03/30/2016] [Accepted: 04/05/2016] [Indexed: 01/11/2023]
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2
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Development of Monolithic Column Materials for the Separation and Analysis of Glycans. CHROMATOGRAPHY 2015. [DOI: 10.3390/chromatography2010020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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3
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Switzar L, Giera M, Niessen WMA. Protein Digestion: An Overview of the Available Techniques and Recent Developments. J Proteome Res 2013; 12:1067-77. [DOI: 10.1021/pr301201x] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Linda Switzar
- AIMMS Division of BioMolecular
Analysis, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Martin Giera
- Division of Molecular Cell Physiology,
Faculty of Earth and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
- Biomolecular Mass Spectrometry
Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Wilfried M. A. Niessen
- AIMMS Division of BioMolecular
Analysis, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
- hyphen MassSpec, de Wetstraat 8, 2332 XT Leiden, The Netherlands
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Gan J, Zhu J, Yan G, Liu Y, Yang P, Liu B. Periodic mesoporous organosilica as a multifunctional nanodevice for large-scale characterization of membrane proteins. Anal Chem 2012; 84:5809-15. [PMID: 22663254 DOI: 10.1021/ac301146a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A versatile protocol has been developed for large-scale characterization of hydrophobic membrane proteins based on the periodic mesoporous organosilica (PMO) acting as both an extractor for hydrophobic substrate capture and a nanoreactor for efficient in situ digestion. With introduction of organic groups in the pore frameworks and the presence of hydrophilic silanol groups on the surface, PMO can be well-dispersed into not only an organic solution to concentrate the dissolved membrane proteins but also an aqueous solution containing enzymes for sequential rapid proteolysis in the nanopores. The unique amphiphilic property of PMO ensures a facile switch in different solutions to realize the processes of substrate dissolution, enrichment, and digestion effectively. Furthermore, this novel PMO-assisted protocol has been successfully applied for identification of complex membrane proteins extracted from mouse liver as proof of general applicability.
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Affiliation(s)
- Jinrui Gan
- Department of Chemistry, Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China
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5
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Kool J, Jonker N, Irth H, Niessen WMA. Studying protein-protein affinity and immobilized ligand-protein affinity interactions using MS-based methods. Anal Bioanal Chem 2011; 401:1109-25. [PMID: 21755271 PMCID: PMC3151372 DOI: 10.1007/s00216-011-5207-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 06/12/2011] [Accepted: 06/24/2011] [Indexed: 12/31/2022]
Abstract
This review discusses the most important current methods employing mass spectrometry (MS) analysis for the study of protein affinity interactions. The methods are discussed in depth with particular reference to MS-based approaches for analyzing protein-protein and protein-immobilized ligand interactions, analyzed either directly or indirectly. First, we introduce MS methods for the study of intact protein complexes in the gas phase. Next, pull-down methods for affinity-based analysis of protein-protein and protein-immobilized ligand interactions are discussed. Presently, this field of research is often called interactomics or interaction proteomics. A slightly different approach that will be discussed, chemical proteomics, allows one to analyze selectivity profiles of ligands for multiple drug targets and off-targets. Additionally, of particular interest is the use of surface plasmon resonance technologies coupled with MS for the study of protein interactions. The review addresses the principle of each of the methods with a focus on recent developments and the applicability to lead compound generation in drug discovery as well as the elucidation of protein interactions involved in cellular processes. The review focuses on the analysis of bioaffinity interactions of proteins with other proteins and with ligands, where the proteins are considered as the bioactives analyzed by MS.
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Affiliation(s)
- Jeroen Kool
- BioMolecular Analysis, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, Amsterdam, The Netherlands.
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6
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Rietschel B, Bornemann S, Arrey TN, Baeumlisberger D, Karas M, Meyer B. Membrane protein analysis using an improved peptic in-solution digestion protocol. Proteomics 2010; 9:5553-7. [PMID: 20017156 DOI: 10.1002/pmic.200900532] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In the proteomic analysis of membrane proteins, less-specific proteases have become a promising tool to overcome fundamental limitations of trypsin with its unique specificity for basic residues. Pepsin is well-known to be utilized for specific applications that require acidic conditions, but in terms of membrane protein identification and characterization, it has been disregarded for the most part. This work presents an optimization of an existing peptic digest protocol for the analysis of membrane proteins using bacteriorhodopsin from purple membranes as reference.
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Affiliation(s)
- Benjamin Rietschel
- Cluster of Excellence Macromolecular Complexes, Institute for Pharmaceutical Chemistry, Goethe-University, Frankfurt am Main, Germany
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Cingöz A, Hugon-Chapuis F, Pichon V. Total on-line analysis of a target protein from plasma by immunoextraction, digestion and liquid chromatography–mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 878:213-21. [DOI: 10.1016/j.jchromb.2009.07.032] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Revised: 07/17/2009] [Accepted: 07/27/2009] [Indexed: 10/20/2022]
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8
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Martha CT, Elders N, Krabbe JG, Kool J, Niessen WMA, Orru RVA, Irth H. Online Screening of Homogeneous Catalyst Performance using Reaction Detection Mass Spectrometry. Anal Chem 2008; 80:7121-7. [DOI: 10.1021/ac801003h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cornelius T. Martha
- Department of Analytical Chemistry and Applied Spectroscopy and Department of Organic and Inorganic Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Niels Elders
- Department of Analytical Chemistry and Applied Spectroscopy and Department of Organic and Inorganic Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Johannes G. Krabbe
- Department of Analytical Chemistry and Applied Spectroscopy and Department of Organic and Inorganic Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Jeroen Kool
- Department of Analytical Chemistry and Applied Spectroscopy and Department of Organic and Inorganic Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Wilfried M. A. Niessen
- Department of Analytical Chemistry and Applied Spectroscopy and Department of Organic and Inorganic Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Romano V. A. Orru
- Department of Analytical Chemistry and Applied Spectroscopy and Department of Organic and Inorganic Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Hubertus Irth
- Department of Analytical Chemistry and Applied Spectroscopy and Department of Organic and Inorganic Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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Geiser L, Eeltink S, Svec F, Fréchet JMJ. In-line system containing porous polymer monoliths for protein digestion with immobilized pepsin, peptide preconcentration and nano-liquid chromatography separation coupled to electrospray ionization mass spectroscopy. J Chromatogr A 2008; 1188:88-96. [PMID: 18342870 PMCID: PMC2435401 DOI: 10.1016/j.chroma.2008.02.075] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2007] [Revised: 02/10/2008] [Accepted: 02/15/2008] [Indexed: 10/22/2022]
Abstract
The use of two different monoliths located in capillaries for on-line protein digestion, preconcentration of peptides and their separation has been demonstrated. The first monolith was used as support for covalent immobilization of pepsin. This monolith with well-defined porous properties was prepared by in situ copolymerization of 2-vinyl-4,4-dimethylazlactone and ethylene dimethacrylate. The second, poly(lauryl methacrylate-co-ethylene dimethacrylate) monolith with a different porous structure served for the preconcentration of peptides from the digest and their separation in reversed-phase liquid chromatography mode. The top of the separation capillary was used as a preconcentrator, thus enabling the digestion of very dilute solutions of proteins in the bioreactor and increasing the sensitivity of the mass spectrometric detection of the peptides using a time-of-flight mass spectrometer with electrospray ionization. Myoglobin, albumin, and hemoglobin were digested to demonstrate feasibility of the concept of using the two monoliths in-line. Successive protein injections confirmed both the repeatability of the results and the ability to reuse the bioreactor for at least 20 digestions.
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Affiliation(s)
- Laurent Geiser
- Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA
| | - Sebastiaan Eeltink
- Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA
| | - Frantisek Svec
- The Molecular Foundry, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8139, USA
| | - Jean M. J. Fréchet
- Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA
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Hoos JS, Damsten MC, de Vlieger JSB, Commandeur JNM, Vermeulen NPE, Niessen WMA, Lingeman H, Irth H. Automated detection of covalent adducts to human serum albumin by immunoaffinity chromatography, on-line solution phase digestion and liquid chromatography–mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 859:147-56. [PMID: 17913598 DOI: 10.1016/j.jchromb.2007.09.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Revised: 09/05/2007] [Accepted: 09/12/2007] [Indexed: 01/09/2023]
Abstract
A generic method for the detection of covalent adducts to the cysteine-34 residue of human serum albumin (HSA) has been developed, based on an on-line combination of immunoaffinity chromatography for selective sample pre-treatment, solution phase digestion, liquid chromatography and tandem mass spectrometry. Selective anti-HSA antibodies immobilized on agarose were used for sample pre-concentration and purification of albumin from the chemically produced alkylated HSA. After elution, HSA and HSA adducts are mixed with pronase and directed to a reaction capillary kept at a digestion temperature of 70 degrees C. The digestion products were trapped on-line on a C18 SPE cartridge. The peptides were separated on a reversed-phase column using a gradient of organic modifier and subsequently detected using tandem mass spectrometry. Modified albumin samples consisted of synthetically alkylated HSA by the reactive metabolite of acetaminophen, N-acetyl-p-benzoquinoneimine (NAPQI), and using the alkylating agent 1-chloro-2,4-dinitrobenzene (CDNB) as reference. The resulting mixture of alkylated versus non-modified albumin has been applied to the on-line system, and alkylation of HSA is revealed by the detection of the modified marker tetra-peptide glutamine-cysteine-proline-phenylalanine (QCPF) adducts NAPQI-QCPF and CDNB-QCPF. Detection of alkylated species was enabled by the use of data comparison algorithms to distinguish between unmodified and modified HSA samples. The in-solution digestion proved to be a useful tool for enabling fast (less than 2 min) and reproducible on-line digestion of HSA. A detection limit of 1.5 micromol/L of modified HSA could be obtained by applying 10 microL of NAPQI-HSA sample.
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Affiliation(s)
- Johannes S Hoos
- Vrije Universiteit Amsterdam, Faculty of Sciences, Section Analytical Chemistry & Applied Spectroscopy, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
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